PDB Short entry for 4AR5 HEADER ELECTRON TRANSPORT 20-APR-12 4AR5 TITLE X-RAY CRYSTALLOGRAPHIC STRUCTURE OF THE OXIDISED FORM PERDEUTERATED TITLE 2 PYROCOCCUS FURIOSUS RUBREDOXIN IN D2O AT 295K (IN QUARTZ CAPILLARY) TITLE 3 TO 1.00 ANGSTROM RESOLUTION. COMPND MOL_ID: 1; COMPND 2 MOLECULE: RUBREDOXIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RD; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: OXIDISED STATE (FE III) SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 3 ORGANISM_TAXID: 2261; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PET28A KEYWDS ELECTRON TRANSPORT, PERDEUTERATED, AMBIENT CAPILLARY EXPDTA X-RAY DIFFRACTION AUTHOR M.G.CUYPERS,S.A.MASON,M.P.BLAKELEY,E.P.MITCHELL,M.HAERTLEIN, AUTHOR 2 V.T.FORSYTH REVDAT 2 30-JAN-13 4AR5 1 JRNL REMARK REVDAT 1 19-DEC-12 4AR5 0 JRNL AUTH M.G.CUYPERS,S.A.MASON,M.P.BLAKELEY,E.P.MITCHELL,M.HAERTLEIN, JRNL AUTH 2 V.T.FORSYTH JRNL TITL NEAR-ATOMIC RESOLUTION NEUTRON CRYSTALLOGRAPHY ON JRNL TITL 2 PERDEUTERATED PYROCOCCUS FURIOSUS RUBREDOXIN: IMPLICATION JRNL TITL 3 OF HYDRONIUM IONS AND PROTONATION EQUILIBRIA AND HYDRONIUM JRNL TITL 4 IONS IN REDOX CHANGES JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 52 1022 2013 JRNL REFN ISSN 1433-7851 JRNL PMID 23225503 JRNL DOI 10.1002/ANIE.201207071 REMARK 2 REMARK 2 RESOLUTION. 1.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.000 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.540 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.36 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.92 REMARK 3 NUMBER OF REFLECTIONS : 28386 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.1099 REMARK 3 R VALUE (WORKING SET) : 0.1095 REMARK 3 FREE R VALUE : 0.1189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.1 REMARK 3 FREE R VALUE TEST SET COUNT : 1439 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 27.5504 - 2.1541 0.89 2671 139 0.1296 0.1270 REMARK 3 2 2.1541 - 1.7099 0.93 2661 142 0.0912 0.1122 REMARK 3 3 1.7099 - 1.4938 0.96 2707 142 0.0790 0.1009 REMARK 3 4 1.4938 - 1.3572 0.96 2727 131 0.0821 0.0980 REMARK 3 5 1.3572 - 1.2599 0.95 2651 137 0.0892 0.1006 REMARK 3 6 1.2599 - 1.1856 0.98 2710 149 0.0926 0.1086 REMARK 3 7 1.1856 - 1.1262 0.99 2766 160 0.0963 0.1103 REMARK 3 8 1.1262 - 1.0772 0.99 2736 143 0.1131 0.1135 REMARK 3 9 1.0772 - 1.0357 0.95 2629 142 0.1596 0.1519 REMARK 3 10 1.0357 - 1.0000 0.98 2689 154 0.2001 0.2243 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.60 REMARK 3 K_SOL : 0.500 REMARK 3 B_SOL : 104.285 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.06 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 8.98 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.15 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.2004 REMARK 3 B22 (A**2) : -0.1398 REMARK 3 B33 (A**2) : -0.0606 REMARK 3 B12 (A**2) : 0.0000 REMARK 3 B13 (A**2) : 0.0000 REMARK 3 B23 (A**2) : 0.0000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 479 REMARK 3 ANGLE : 1.229 657 REMARK 3 CHIRALITY : 0.079 64 REMARK 3 PLANARITY : 0.008 90 REMARK 3 DIHEDRAL : 11.701 186 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: CRYSTAL SEALED IN A QUARTZ CAPILLARY REMARK 3 FOR 295K X-RAY DATA COLLECTION ON 2 DIFFERENT ZONES REMARK 3 OVER TOTAL 90 DEGREES OSCILLATION ROTATION. REMARK 4 REMARK 4 4AR5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-APR-12. REMARK 100 THE PDBE ID CODE IS EBI-52085. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAR-11 REMARK 200 TEMPERATURE (KELVIN) : 295 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.77 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL (PILATUS 6M) REMARK 200 DETECTOR MANUFACTURER : DECTRIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28427 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.00 REMARK 200 RESOLUTION RANGE LOW (A) : 35.32 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 3.3 REMARK 200 R MERGE (I) : 0.04 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.40 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.1 REMARK 200 R MERGE FOR SHELL (I) : 0.47 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.10 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: ISOMORPHOUS REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 100 K 0.80 A RESOLUTION OXIDISED REMARK 200 PF RUBREDOXIN STRUCTURE. REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.4 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 17.18050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 21.99650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.65800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 21.99650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.18050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 17.65800 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 18 68.39 -153.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 DOD A2138 DISTANCE = 7.3 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A1054 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 5 SG REMARK 620 2 CYS A 41 SG 104.1 REMARK 620 3 CYS A 8 SG 113.0 113.8 REMARK 620 4 CYS A 38 SG 111.3 112.0 102.9 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE A1054 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BQ8 RELATED DB: PDB REMARK 900 RUBREDOXIN (METHIONINE MUTANT) FROM PYROCOCCUS FURIOSUS REMARK 900 RELATED ID: 1BQ9 RELATED DB: PDB REMARK 900 RUBREDOXIN (FORMYL METHIONINE MUTANT) FROM PYROCOCCUS REMARK 900 FURIOSUS REMARK 900 RELATED ID: 1BRF RELATED DB: PDB REMARK 900 RUBREDOXIN (WILD TYPE) FROM PYROCOCCUS FURIOSUS REMARK 900 RELATED ID: 1CAA RELATED DB: PDB REMARK 900 RUBREDOXIN (OXIDIZED) REMARK 900 RELATED ID: 1CAD RELATED DB: PDB REMARK 900 RUBREDOXIN (REDUCED) REMARK 900 RELATED ID: 1IU5 RELATED DB: PDB REMARK 900 X-RAY CRYSTAL STRUCTURE OF THE RUBREDOXIN MUTANT REMARK 900 FROMPYROCOCCUS FURIOSUS REMARK 900 RELATED ID: 1IU6 RELATED DB: PDB REMARK 900 NEUTRON CRYSTAL STRUCTURE OF THE RUBREDOXIN MUTANT REMARK 900 FROMPYROCOCCUS FURIOSUS REMARK 900 RELATED ID: 1QCV RELATED DB: PDB REMARK 900 RUBREDOXIN VARIANT (PFRD-XC4) FOLDS WITHOUT IRON REMARK 900 RELATED ID: 1RWD RELATED DB: PDB REMARK 900 BACKBONE NMR STRUCTURE OF A MUTANT P. FURIOSUS REMARK 900 RUBREDOXINUSING RESIDUAL DIPOLAR COUPLINGS REMARK 900 RELATED ID: 1VCX RELATED DB: PDB REMARK 900 NEUTRON CRYSTAL STRUCTURE OF THE WILD TYPE RUBREDOXIN REMARK 900 FROMPYROCOCCUS FURIOSUS AT 1.5A RESOLUTION REMARK 900 RELATED ID: 1ZRP RELATED DB: PDB REMARK 900 RUBREDOXIN (ZN-SUBSTITUTED) (NMR, 40 STRUCTURES) REMARK 900 RELATED ID: 4AR3 RELATED DB: PDB REMARK 900 NEAR-ATOMIC RESOLUTION NEUTRON CRYSTALLOGRAPHY ON THE REMARK 900 OXIDISED FORM PERDEUTERATED PYROCOCCUS FURIOSUS RUBREDOXIN. REMARK 900 RELATED ID: 4AR4 RELATED DB: PDB REMARK 900 NEUTRON CRYSTALLOGRAPHIC STRUCTURE OF THE REDUCED FORM REMARK 900 PERDEUTERATED PYROCOCCUS FURIOSUS RUBREDOXIN TO 1.38 REMARK 900 ANGSTROMS RESOLUTION. REMARK 900 RELATED ID: 4AR6 RELATED DB: PDB REMARK 900 X-RAY CRYSTALLOGRAPHIC STRUCTURE OF THE REDUCED FORM REMARK 900 PERDEUTERATED PYROCOCCUS FURIOSUS RUBREDOXIN AT 295 K ( REMARK 900 IN QUARTZ CAPILLARY) TO 0.92 ANGSTROMS RESOLUTION. DBREF 4AR5 A 0 53 UNP P24297 RUBR_PYRFU 1 54 SEQRES 1 A 54 MET ALA LYS TRP VAL CYS LYS ILE CYS GLY TYR ILE TYR SEQRES 2 A 54 ASP GLU ASP ALA GLY ASP PRO ASP ASN GLY ILE SER PRO SEQRES 3 A 54 GLY THR LYS PHE GLU GLU LEU PRO ASP ASP TRP VAL CYS SEQRES 4 A 54 PRO ILE CYS GLY ALA PRO LYS SER GLU PHE GLU LYS LEU SEQRES 5 A 54 GLU ASP HET FE A1054 1 HETNAM FE FE (III) ION FORMUL 2 FE FE 3+ FORMUL 3 DOD *135(D2 O) HELIX 1 1 PRO A 19 GLY A 22 5 4 HELIX 2 2 LYS A 28 LEU A 32 5 5 SHEET 1 AA 3 ILE A 11 ASP A 13 0 SHEET 2 AA 3 LYS A 2 CYS A 5 -1 O TRP A 3 N TYR A 12 SHEET 3 AA 3 PHE A 48 LYS A 50 -1 O GLU A 49 N VAL A 4 LINK FE FE A1054 SG CYS A 5 1555 1555 2.29 LINK FE FE A1054 SG CYS A 41 1555 1555 2.27 LINK FE FE A1054 SG CYS A 8 1555 1555 2.27 LINK FE FE A1054 SG CYS A 38 1555 1555 2.31 SITE 1 AC1 4 CYS A 5 CYS A 8 CYS A 38 CYS A 41 CRYST1 34.361 35.316 43.993 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.029103 0.000000 0.000000 0.00000 SCALE2 0.000000 0.028316 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022731 0.00000